HEADER SIGNALING PROTEIN 29-JUN-22 8DIK TITLE REDOX PROPERTIES AND PAS DOMAIN STRUCTURE OF THE E. COLI ENERGY SENSOR TITLE 2 AER INDICATE A MULTI-STATE SENSING MECHANISM COMPND MOL_ID: 1; COMPND 2 MOLECULE: AEROTAXIS RECEPTOR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PAS DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ENERGY SENSING CHEMOTAXIS PAS DOMAIN AEROTAXIS, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.MASCHMANN,T.K.CHUA,B.R.CRANE REVDAT 3 25-OCT-23 8DIK 1 REMARK REVDAT 2 30-NOV-22 8DIK 1 JRNL REVDAT 1 09-NOV-22 8DIK 0 JRNL AUTH Z.A.MASCHMANN,T.K.CHUA,S.CHANDRASEKARAN,H.IBANEZ,B.R.CRANE JRNL TITL REDOX PROPERTIES AND PAS DOMAIN STRUCTURE OF THE ESCHERICHIA JRNL TITL 2 COLI ENERGY SENSOR AER INDICATE A MULTISTATE SENSING JRNL TITL 3 MECHANISM. JRNL REF J.BIOL.CHEM. V. 298 02598 2022 JRNL REFN ESSN 1083-351X JRNL PMID 36252616 JRNL DOI 10.1016/J.JBC.2022.102598 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 120.23 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 9349 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.261 REMARK 3 R VALUE (WORKING SET) : 0.254 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 938 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.1597 - 4.5879 0.89 1235 133 0.2676 0.2538 REMARK 3 2 4.5879 - 3.6430 0.89 1218 132 0.2254 0.2919 REMARK 3 3 3.6430 - 3.1830 0.90 1198 133 0.2636 0.2581 REMARK 3 4 3.1830 - 2.8921 0.90 1214 138 0.2536 0.3110 REMARK 3 5 2.8921 - 2.6849 0.90 1198 130 0.2776 0.2724 REMARK 3 6 2.6849 - 2.5267 0.90 1210 133 0.2864 0.2695 REMARK 3 7 2.5267 - 2.4002 0.87 1137 135 0.3012 0.3530 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.000 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 2074 REMARK 3 ANGLE : 0.523 2837 REMARK 3 CHIRALITY : 0.039 302 REMARK 3 PLANARITY : 0.004 348 REMARK 3 DIHEDRAL : 4.897 1177 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8DIK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1000266681. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.968 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9349 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 48.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.16800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: ALPHAFOLD PREDICTION WITH FAD COORDINATES FROM REMARK 200 2GJ3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% (W/V) PEG-3000, 100 MM TRIS PH REMARK 280 7.00, 150 MM NACL, 20% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 31.47350 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 THR B 8 REMARK 465 GLN B 9 REMARK 465 GLN B 10 REMARK 465 ASN B 11 REMARK 465 THR B 12 REMARK 465 PRO B 13 REMARK 465 LEU B 14 REMARK 465 ALA B 15 REMARK 465 ASP B 16 REMARK 465 ASP B 17 REMARK 465 THR B 18 REMARK 465 LYS B 131 REMARK 465 ALA B 132 REMARK 465 LEU B 133 REMARK 465 ASN B 134 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 107 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 133 -65.13 -102.86 REMARK 500 ASP B 25 -159.62 -106.00 REMARK 500 ARG B 87 -156.77 -78.79 REMARK 500 ASN B 89 4.12 -63.68 REMARK 500 VAL B 126 -18.02 -150.37 REMARK 500 REMARK 500 REMARK: NULL DBREF 8DIK A 8 134 UNP P50466 AER_ECOLI 8 134 DBREF 8DIK B 8 134 UNP P50466 AER_ECOLI 8 134 SEQADV 8DIK GLY A 28 UNP P50466 SER 28 ENGINEERED MUTATION SEQADV 8DIK VAL A 65 UNP P50466 ALA 65 ENGINEERED MUTATION SEQADV 8DIK VAL A 99 UNP P50466 ALA 99 ENGINEERED MUTATION SEQADV 8DIK GLY B 28 UNP P50466 SER 28 ENGINEERED MUTATION SEQADV 8DIK VAL B 65 UNP P50466 ALA 65 ENGINEERED MUTATION SEQADV 8DIK VAL B 99 UNP P50466 ALA 99 ENGINEERED MUTATION SEQRES 1 A 127 THR GLN GLN ASN THR PRO LEU ALA ASP ASP THR THR LEU SEQRES 2 A 127 MET SER THR THR ASP LEU GLN GLY TYR ILE THR HIS ALA SEQRES 3 A 127 ASN ASP THR PHE VAL GLN VAL SER GLY TYR THR LEU GLN SEQRES 4 A 127 GLU LEU GLN GLY GLN PRO HIS ASN MET VAL ARG HIS PRO SEQRES 5 A 127 ASP MET PRO LYS ALA VAL PHE ALA ASP MET TRP PHE THR SEQRES 6 A 127 LEU LYS LYS GLY GLU PRO TRP SER GLY ILE VAL LYS ASN SEQRES 7 A 127 ARG ARG LYS ASN GLY ASP HIS TYR TRP VAL ARG ALA ASN SEQRES 8 A 127 VAL VAL PRO MET VAL ARG GLU GLY LYS ILE SER GLY TYR SEQRES 9 A 127 MET SER ILE ARG THR ARG ALA THR ASP GLU GLU ILE ALA SEQRES 10 A 127 ALA VAL GLU PRO LEU TYR LYS ALA LEU ASN SEQRES 1 B 127 THR GLN GLN ASN THR PRO LEU ALA ASP ASP THR THR LEU SEQRES 2 B 127 MET SER THR THR ASP LEU GLN GLY TYR ILE THR HIS ALA SEQRES 3 B 127 ASN ASP THR PHE VAL GLN VAL SER GLY TYR THR LEU GLN SEQRES 4 B 127 GLU LEU GLN GLY GLN PRO HIS ASN MET VAL ARG HIS PRO SEQRES 5 B 127 ASP MET PRO LYS ALA VAL PHE ALA ASP MET TRP PHE THR SEQRES 6 B 127 LEU LYS LYS GLY GLU PRO TRP SER GLY ILE VAL LYS ASN SEQRES 7 B 127 ARG ARG LYS ASN GLY ASP HIS TYR TRP VAL ARG ALA ASN SEQRES 8 B 127 VAL VAL PRO MET VAL ARG GLU GLY LYS ILE SER GLY TYR SEQRES 9 B 127 MET SER ILE ARG THR ARG ALA THR ASP GLU GLU ILE ALA SEQRES 10 B 127 ALA VAL GLU PRO LEU TYR LYS ALA LEU ASN HET FAD A 501 53 HET FAD B 201 53 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 3 FAD 2(C27 H33 N9 O15 P2) FORMUL 5 HOH *52(H2 O) HELIX 1 AA1 ASN A 34 GLY A 42 1 9 HELIX 2 AA2 THR A 44 GLN A 49 1 6 HELIX 3 AA3 PRO A 62 LYS A 75 1 14 HELIX 4 AA4 THR A 119 LYS A 131 1 13 HELIX 5 AA5 ASN B 34 GLY B 42 1 9 HELIX 6 AA6 THR B 44 GLN B 49 1 6 HELIX 7 AA7 PRO B 62 LYS B 74 1 13 HELIX 8 AA8 THR B 119 ALA B 125 1 7 HELIX 9 AA9 VAL B 126 TYR B 130 5 5 SHEET 1 AA1 5 ILE A 30 ALA A 33 0 SHEET 2 AA1 5 THR A 19 THR A 24 -1 N THR A 23 O THR A 31 SHEET 3 AA1 5 LYS A 107 ARG A 117 -1 O ARG A 115 N LEU A 20 SHEET 4 AA1 5 HIS A 92 ARG A 104 -1 N MET A 102 O GLY A 110 SHEET 5 AA1 5 TRP A 79 ARG A 86 -1 N VAL A 83 O VAL A 95 SHEET 1 AA2 5 ILE B 30 ALA B 33 0 SHEET 2 AA2 5 LEU B 20 ASP B 25 -1 N THR B 23 O THR B 31 SHEET 3 AA2 5 LYS B 107 ARG B 117 -1 O ARG B 115 N LEU B 20 SHEET 4 AA2 5 HIS B 92 ARG B 104 -1 N ARG B 96 O THR B 116 SHEET 5 AA2 5 TRP B 79 ARG B 86 -1 N VAL B 83 O VAL B 95 CRYST1 24.592 62.947 78.013 90.00 89.96 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.040664 0.000000 -0.000029 0.00000 SCALE2 0.000000 0.015886 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012818 0.00000